Multi-scale modeling of gas transport through channels in living cells

通过活细胞通道进行气体传输的多尺度建模

• 批准号: 9198249
• 负责人: Walter F Boron
• 金额: $ 57.65万
• 依托单位: CASE WESTERN RESERVE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-01-01 至 2019-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9198249
• 关键词: AQP1 gene; Acid-Base Equilibrium; Acids; Address; Ammonia; Bicarbonates; Binding; Biological; Boron; Caliber; Carbon Dioxide; Cell Respiration; Cell membrane; Cell physiology; Cell surface; Cells; Chemicals; Chronic Obstructive Airway Disease; Complex; Computer Simulation; Crystallization; Diffuse; Diffusion; Disease; Electrodes; Electrophysiology (science); Enzymes; Equilibrium; Erythrocytes; Event; Failure; Gases; Health; Hyperammonemia; Interstitial Lung Diseases; Ion Channel; Ligands; Lipid Bilayers; Lipids; Liver Failure; Macaca mulatta; Measurement; Measures; Membrane; Membrane Lipids; Metals; Methodology; Microelectrodes; Microscopic; Modeling; Modification; Molecular; Molecular Probes; Monitor; Movement; Mutate; Mutation; Oocytes; Optical Methods; Pathologic; Pathway interactions; Permeability; Pharmacology; Phase; Physiological; Physiological Processes; Physiology; Play; Process; Proteins; Public Health; Reaction; Refuse Disposal; Rest; Role; Running; Signal Transduction; Surface; Testing; Touch sensation; Urea; Validation; Work; Xenopus oocyte; airway epithelium; base; carbonate dehydratase; data integration; design; experimental study; insight; mathematical model; models and simulation; molecular dynamics; multi-scale modeling; mutant; novel; operation; public health relevance; simulation; urea transporter; water channel

DESCRIPTION (provided by applicant): The transport of gases across cell membranes is one of the most fundamental of physiological processes-O2 for oxidative metabolism, CO2 for acid-base balance, and NH3 for waste disposal. CO2 retention and hyperammonemia are key components of diseases that are major public health concerns. The traditional dogma had been that all gases cross all cell membranes by diffusing through membrane lipid. However, some membranes are gas impermeable and require protein 'gas channels' such as the aquaporins AQP1 (abundant in red blood cells) and AQP5 (abundant in airway epithelia) to conduct gases such as CO2 and NH3. Movement of these gases through AQPs results in a disturbance of pH in microdomains around the channels that we can measure using a pH microelectrode. However, the mechanism of gas conduction is poorly understood. Molecular dynamic simulations, measurements of the pH beneath an electrode touching the surface (pHS) of a model spherical cell (Xenopus oocytes), as well as a mathematical model addressing these pHS changes have provided the first insights into CO2 and NH3 movement through channels. However, a fundamental understanding of such movements across cell membranes requires more advanced multi-scale mathematical models (microscopic, mesoscopic, sub-macroscopic and macroscopic) in order to elucidate mechanisms of gas permeation in normal and pathological states. The PIs (Drs. Boron, Somersalo, and Tajkhorshid) propose to combine state-of-the-art molecular dynamic simulations and computational modeling with novel experimental studies to develop a predictive mathematical model for permeation of various gases across diverse cell membranes of different protein composition, based on integration of data from complementary methodologies across a range of spatial and temporal scales. We will run molecular dynamic simulations of NH3 and CO2 passage through wild-type, mutant, chemically modified, and metal-bound aquaporins in Aim 1 to predict single channel permeabilities (microscopic scale) that will inform the modeling in Aim 2 and cell physiology in Aim 3. In Aim 2, we will create new computational models of gas transport through single and multiple aquaporins in a lipid bilayer (mesoscopic scale), beneath the pHS electrode (sub-macroscopic scale) and in the whole cell (macroscopic scale). Finally in Aim 3, informed by Aims 1 and 2, we will validate the simulations and models in oocytes using electrophysiological and optical methods.

描述(申请人提供)：跨细胞膜的气体运输是最基本的生理过程之一-O2用于氧化代谢，CO2用于酸碱平衡，NH3用于废物处理。二氧化碳滞留和高氨血症是引起重大公共卫生问题的疾病的关键组成部分。传统的教条是所有的气体都通过膜脂扩散穿过所有的细胞膜。然而，一些膜是不透气的，需要蛋白质“气体通道”，如水通道蛋白AQP1(丰富的红细胞)和AQP5(丰富的呼吸道上皮细胞)来传导气体，如二氧化碳和氨。这些气体通过水通道蛋白的运动导致通道周围微区的pH值扰动，我们可以使用pH值微电极进行测量。然而，人们对气体传导的机制知之甚少。分子动力学模拟，对接触模型球形细胞(非洲爪哇卵母细胞)表面的电极(PHS)下的pH的测量，以及解决这些PHS变化的数学模型，提供了对二氧化碳和NH3在通道中移动的第一次洞察。然而，要从根本上理解这种跨细胞膜的运动，需要更先进的多尺度数学模型(微观、介观、亚宏观和宏观)，以阐明正常和病理状态下气体渗透的机制。PIs(Boron、Somersalo和Tajkhorshid博士)建议将最先进的分子动力学模拟和计算建模与新的实验研究相结合，基于在一系列空间和时间尺度上的互补方法的数据集成，开发不同气体通过不同蛋白质组成的不同细胞膜的预测数学模型。在目标1中，我们将对NH3和CO2通过野生型、突变型、化学修饰和金属结合的水通道蛋白进行分子动力学模拟，以预测单通道渗透率(微观尺度)，这将为目标2中的建模和目标3中的细胞生理学提供信息。在目标2中，我们将创建新的计算模型，在脂质双层(介观尺度)、PHS电极下(亚宏观尺度)和整个细胞(宏观尺度)中气体通过单个和多个水通道蛋白。最后，在目标3中，在目标1和目标2的启发下，我们将使用电生理和光学方法在卵母细胞中验证模拟和模型。